eDNA - The Non-Invasive Option for Marine Species Research
Updated: Dec 18, 2020
In the past, oceanic researchers had to use rough, and often deadly, methods to acquire specimen samples from the ocean to study. Although, thanks to better quality marine technology like high definition cameras, the scientific landscape is changing and oceanic species are beginning to be described virtually; genetic sampling still plays one of the most important roles for species classification and description. When scientists are "lucky", they find dead specimens stranded on a beach, or perhaps some remains of a specimen during a dive (which is also cool because you can see how the ecosystem handles remains), and from these specimens they can take samples and do their work. But, this isn't ideal for many reasons - samples ruin faster, they might be mixed with things that will make analysis difficult, its dangerous, and sometimes it's a little gross.
Modern marine researchers refrain from using harmful methods as much as they can; research in general has become gentler with nature, not just out of empathy but because the results usually turn out way better. For example, stressed specimens are more likely to flee, and therefore are less likely to ever appear for marine researchers again. This is a BIG challenge when dealing with intrinsically elusive creatures, like the Perrins beaked whale or Giant Squid. To inspect these and other delicate creatures, modern marine researchers have turned to using eDNA to reduce stress on their target specimens. The eDNA method is fairly new - although the concept has been around for a while and rudimentary versions of it received some love in the soil science industry. With recent improvements in information technology, the usage and efficacy of eDNA has risen pleasantly.
How Does eDNA Work?
We were able to get in-touch with Jan Pawlowski, CSO of ID-Gene Ecodiagnostics, a Swiss company offering a full service in eDNA biomonitoring, from eDNA sampling to high throughput sequencing and bioinformatics. It is specialized in environmental impact assessment of marine industries but it also performs analysis of biological quality of water and sediments in rivers and lakes, as well as the detection of aquatic pathogens, parasites and invasive species. Pawlowski is also a professor at the University of Geneva, Department of Genetics and Evolution, who has been working with eDNA for quite a while now, and has published numerous papers on the subject. He was able to define the usefulness of eDNA, like with the recent example of a new species of whale where genetic samples were collected using this method, but took it a step further by describing the miracle of detecting a species without even seeing it, stating "there is no need to spot an animal to attest its presence based on its DNA traces left in the water".
DNA collection using eDNA has seen success all over the world, but the efficiency could be impacted depending on the usage. For instance, with marine studies, limiting factors could include: the amount of water collected, the amount of water that can be analyzed, the DNA production of the target species (mucus, skin shed, urine), how degrading the environment is, and the database quality.
Speaking of genetic databases, Pawlowski was able to share with us some of the more common databases in use and who produces them. The largest database appears to be the U.S. National Center of Biotechnology Information (NCBI) "Genbank", which exchanges data with two other major genetic institutions (DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA)) and publishes an updated database every two months. Other databases include the SILVA database, which appears to be good for microbe DNA sequencing, and BOLD Systems. While these databases provide a TON of info - as you could imagine, new DNA sequences and information are being collected every day.
That being said, everyone has their databases to choose from. As for eDNA collection and testing methodology; that varies depending who you are, where you're doing it, and what you're targeting. There is consensus regarding most methods; which are the most efficient, which make the most sense for the DNA capture goal - but standardization is forthcoming due to the recent nature of eDNA. eDNA can be used in a large array of applications, including studies on prevalence, environmental surveys and impacts, detection of species, and in multiple mediums such as water, sediment, soil, air, and more. Pawlowski provided a concise report on applicability here.
Work With eDNA?
We also asked Pawlowski about the types of skills and qualifications a person should have if they want to work with eDNA. As you most likely expected, degrees involving biology, especially specialized degrees focusing on a target field, would be required. For eDNA professionals, work history or experience with molecular biology and bioinformatics would be preferred. However, with the constant progression of technology, eDNA applications are becoming increasingly available for other fields such as ecologists and environmental managers.
For more content on marine sciences and interesting articles on methods like eDNA collection, you should seriously consider following TheVast on Twitter and Facebook, and subscribing on Youtube for awesome and interesting videos! To stay connected to important news, subscribe to our newsletter which is distributed bi-weekly!